Therein lies the problem. The 7th arrived a day early. It has been argued that had he scouted Tullock's fork as his orders called for, he'd have arrived on the proper day. But the 7th had found the trail, it led straight across the Wolf mountains to the Little Big Horn, so that scout, which could conceivably alert the Indians to the 7th's presence, was pretty unnecessary, IMO.
Custer's initial plan was to wait in hiding in the Wolf mountains until the next day. But finding that his troops had apparently been found by roaming Indians precipitated the attack to that day (the 25th). This gave him no time for scouting, and his only input on the village came from the Crow's Nest which was over 15 miles away, the camp itself being hid by the hills along the river.
Custer used a plan very similar to his attack on the Washita. It worked there although the unknown additional villages cause complications later that day. This is why he sent Benteen on his scout upstream; to determine whether, again, there were additional villages. Little could he know that those villages were all in one, very large encampment. That just wasn't common on the plains.
Also, neither was the prospect that the Indians would stay and fight instead of flee. Yet, after their fight on the Rosebud a week before, and what with the size of the village (present estimates center around 1800-2000 warriors or fighting age adult men), they felt they could handle anything. However, there was no way Custer could know this although his scouts felt the presentment.
It's not so much that the plan to separate his wings was a bad one. It became untenable because of the terrain, again something Custer had no time to scout. And while Reno was attacking the village in the valley from upstream, and Benteen was dogging it on the backtrail, Custer was trying to find a suitable ford from the eastern hills, fords being few and far between. The layout of the eastern hills really took him out of the action for some time. So, it wasn't the plan as much as topography made that plan useless.
Which is why terrain analysis is a major factor in all military planning to this day. I would assume it would have been then, too, but, as you said, all assumptions based on years of experience pointed to the Indians running rather than fighting.